[DAS] SEVERE: DazzleServerMain: DAS Error

[Warren, Jonathan]

Hi Thomas

Amazingly I do seem to have used the wrong request consistently with the
annotation servers but not with the reference server - I apologise.

We are getting another error with our new annotations to the new
reference server however ?
 

SEVERE: Servlet.service() for servlet DazzleServerMain threw exception
java.lang.IndexOutOfBoundsException: max must exceed min:
min=2147400001, max=-2147467296
        at
org.biojava.bio.symbol.RangeLocation.<init>(RangeLocation.java:61)
        at
org.ensembl.das.GenericSeqFeatureSource$TiledFeatures.<init>(GenericSeqF
eatureSource.java:403)
        at
org.ensembl.das.GenericSeqFeatureSource.getFeatures(GenericSeqFeatureSou
rce.java:225)
        at
org.biojava.servlets.dazzle.DazzleServlet.featuresCommand(DazzleServlet.
java:933)
        at
org.biojava.servlets.dazzle.DazzleServlet.doGet(DazzleServlet.java:257)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:689)
        at javax.servlet.http.HttpServlet.service(HttpServlet.java:802)
        at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(Applica
tionFilterChain.java:237)
        at
org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilt
erChain.java:157)
        at
org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValv
e.java:214)
        at
org.apache.catalina.core.StandardContextValve.invoke(StandardContextValv
e.java:178)
        at
org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java
:126)
        at
org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java
:105)
        at
org.apache.catalina.valves.FastCommonAccessLogValve.invoke(FastCommonAcc
essLogValve.java:481)
        at
org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.
java:107)
        at
org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:1
48)
        at
org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:82
5)
        at
org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.processC
onnection(Http11Protocol.java:731)
        at
org.apache.tomcat.util.net.PoolTcpEndpoint.processSocket(PoolTcpEndpoint
.java:526)
        at
org.apache.tomcat.util.net.LeaderFollowerWorkerThread.runIt(LeaderFollow
erWorkerThread.java:80)
        at
org.apache.tomcat.util.threads.ThreadPool$ControlRunnable.run(ThreadPool
.java:684)
        at java.lang.Thread.run(Thread.java:534)  

-----Original Message-----
From: Thomas Down [mailto:td2 at sanger.ac.uk] 
Sent: Tuesday, February 22, 2005 10:17 PM
To: Warren, Jonathan
Cc: das at biodas.org
Subject: Re: [DAS] SEVERE: DazzleServerMain: DAS Error


On 22 Feb 2005, at 03:35, Warren, Jonathan wrote:

> Can anyone point me in the direction of why I would get the following
> error?
>
> We recently upgraded to the new version of dazzle and our old and new
> data sources now don't work.
>
> The reference servers for ensembl versions 25_34 and 18_34 work fine,
> but our extra annotations in generic feature tables return the 
> following
> errors when a features?segment=1,1000 or something similar is used.
> (They show up as sources just fine).

I think there's an error in the request there.  You can do either:

           features?segment=1      (all features on the sequence named 
"1")

or:

           features?segment=1:1,1000   (features overlapping positions 
1-1000 on "1")

But I don't know of any valid request type which just uses two numbers. 
  The error you're showing comes from the code which parses the 
"segment=" part of the request.

Am I missing something here?

         Thomas.

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